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Report generated at 2020-06-05 16:20:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	82454126	78469500
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79049607	76523645
Mapped(QC-failed)	0	0
% Mapped	95.8700	97.5200
Paired	82454126	78469500
Paired(QC-failed)	0	0
Read1	41227063	39234750
Read1(QC-failed)	0	0
Read2	41227063	39234750
Read2(QC-failed)	0	0
Properly Paired	77667412	74787695
Properly Paired(QC-failed)	0	0
% Properly Paired	94.1900	95.3100
With itself	78281366	75995226
With itself(QC-failed)	0	0
Singletons	768241	528419
Singletons(QC-failed)	0	0
% Singleton	0.9300	0.6700
Diff. Chroms	112902	142328
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	31821468	32771047
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2030894	449973
Paired Opt. Dupes	11545	9923
% Dupes/100	0.0638	0.0137

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31820699	32746475
Distinct Read Pairs	29789857	32297098
One Read Pair	27884242	31857228
Two Read Pairs	1788285	432385
NRF = Distinct/Total	0.9362	0.9863
PBC1 = OnePair/Distinct	0.9360	0.9864
PBC2 = OnePair/TwoPair	15.5927	73.6779

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	59581148	64642148
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59581148	64642148
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59581148	64642148
Paired(QC-failed)	0	0
Read1	29790574	32321074
Read1(QC-failed)	0	0
Read2	29790574	32321074
Read2(QC-failed)	0	0
Properly Paired	59581148	64642148
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59581148	64642148
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	99225
Np	0
N optimal	99225
N conservative	99225
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	115
Corr. Est. Fragment Len.	0.1946
Phantom Peak	50
Corr. Phantom Peak	0.2219
Argmin. Corr.	1500
Min. Corr.	0.1806
NSC	1.0772
RSC	0.3377

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.1681

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.2530
AUC	0.4947
CHANCE divergence	0.1170
Elbow Point	0.0000
JS Distance	0.6239
Synthetic AUC	0.4955
Synthetic Elbow Point	0.1743
Synthetic JS Distance	0.3253